Package index
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ordr
ordr-package
- ordr package
Functions, classes, and methods
Introducing and adapting ordination techniques for the ordr workflow
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lda_ord()
predict(<lda_ord>)
model.frame(<lda_ord>)
- Augmented implementation of linear discriminant analysis
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lra()
print(<lra>)
screeplot(<lra>)
biplot(<lra>)
plot(<lra>)
- Log-ratio analysis
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eigen_ord()
svd_ord()
cmdscale_ord()
cancor_ord()
- Wrappers for lossy ordination methods
Tidy ordination
The ‘tbl_ord’ class wrapper, with methods for accessing components and for querying and manipulating metadata
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recover_rows()
recover_cols()
get_rows()
get_cols()
as.matrix(<tbl_ord>)
recover_inertia()
recover_coord()
get_coord()
get_inertia()
dim(<tbl_ord>)
- Access factors, coordinates, and metadata from ordination objects
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recover_aug_rows()
recover_aug_cols()
recover_aug_coord()
augment_ord()
- Augment factors and coordinates of 'tbl_ord' objects
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tidy(<tbl_ord>)
glance(<tbl_ord>)
fortify(<tbl_ord>)
- Tidiers for 'tbl_ord' objects
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annotation
- Annotate factors of 'tbl_ord' objects
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get_negation()
revert_negation()
negate_ord()
negate_to_first_orthant()
- Negation of ordination axes
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recover_conference()
get_conference()
revert_conference()
confer_inertia()
- Confer inertia to factors of a 'tbl_ord' object
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recover_supp_rows()
recover_supp_cols()
- Supplement 'tbl_ord' objects with new data
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as_tbl_ord()
make_tbl_ord()
is_tbl_ord()
is.tbl_ord()
valid_tbl_ord()
un_tbl_ord()
- A unified ordination object class
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format(<tbl_ord>)
print(<tbl_ord>)
- Format a tbl_ord for printing
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plot(<tbl_ord>)
screeplot(<tbl_ord>)
biplot(<tbl_ord>)
- Plot and biplot methods for 'tbl_ord' objects
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pull_factor()
pull_rows()
pull_cols()
rename_rows()
rename_cols()
select_rows()
select_cols()
mutate_rows()
mutate_cols()
transmute_rows()
transmute_cols()
cbind_rows()
cbind_cols()
left_join_rows()
left_join_cols()
- dplyr verbs for tbl_ord factors
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ordinate()
- Fit an ordination model to a data object
Layered grammar for biplots
Functions to generate and annotate biplots from ‘tbl_ord’ objects, following the layered grammar of graphics
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ggbiplot()
ord_aes()
- Biplots following the grammar of graphics
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coord_scaffold()
- Convenience coordinate system for scaffolding axes
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stat_rows()
stat_cols()
- Render plot elements for one matrix of an ordination
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stat_projection()
- Project rows onto columns or vice-versa
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geom_origin()
geom_unit_circle()
- Marker or unit circle at the origin
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geom_interpolation()
- Render interpolation of new rows from columns (or vice-versa)
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theme_scaffold()
theme_biplot()
- Scaffolding theme
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draw_key_line()
draw_key_crosslines()
draw_key_crosspoint()
- Biplot key drawing functions
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ordr-ggproto
CoordScaffold
GeomInterpolation
GeomOrigin
GeomUnitCircle
StatRows
StatCols
StatProjection
StatRowsDensity2d
StatColsDensity2d
StatRowsDensity2dFilled
StatColsDensity2dFilled
StatRowsEllipse
StatColsEllipse
StatRowsCenter
StatColsCenter
StatRowsStar
StatColsStar
StatRowsChull
StatColsChull
StatRowsPeel
StatColsPeel
StatRowsCone
StatColsCone
StatRowsDepth
StatColsDepth
StatRowsDepthFilled
StatColsDepthFilled
StatRowsScale
StatColsScale
StatRowsSpantree
StatColsSpantree
StatRowsBagplot
StatColsBagplot
StatRowsRule
StatColsRule
StatRowsProjection
StatColsProjection
- ggproto classes created and adapted for ordr
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geom_rows_point()
geom_cols_point()
geom_rows_path()
geom_cols_path()
geom_rows_polygon()
geom_cols_polygon()
geom_rows_contour()
geom_cols_contour()
geom_rows_density_2d()
geom_cols_density_2d()
geom_rows_density_2d_filled()
geom_cols_density_2d_filled()
geom_rows_text()
geom_cols_text()
geom_rows_label()
geom_cols_label()
geom_rows_text_repel()
geom_cols_text_repel()
geom_rows_label_repel()
geom_cols_label_repel()
geom_rows_axis()
geom_cols_axis()
geom_rows_pointranges()
geom_cols_pointranges()
geom_rows_lineranges()
geom_cols_lineranges()
geom_rows_isoline()
geom_cols_isoline()
geom_rows_text_radiate()
geom_cols_text_radiate()
geom_rows_vector()
geom_cols_vector()
geom_rows_bagplot()
geom_cols_bagplot()
geom_rows_rule()
geom_cols_rule()
geom_rows_interpolation()
geom_cols_interpolation()
- Convenience geoms for row and column matrix factors
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stat_rows_density_2d()
stat_cols_density_2d()
stat_rows_density_2d_filled()
stat_cols_density_2d_filled()
stat_rows_ellipse()
stat_cols_ellipse()
stat_rows_center()
stat_cols_center()
stat_rows_star()
stat_cols_star()
stat_rows_chull()
stat_cols_chull()
stat_rows_peel()
stat_cols_peel()
stat_rows_cone()
stat_cols_cone()
stat_rows_depth()
stat_cols_depth()
stat_rows_depth_filled()
stat_cols_depth_filled()
stat_rows_scale()
stat_cols_scale()
stat_rows_spantree()
stat_cols_spantree()
stat_rows_bagplot()
stat_cols_bagplot()
stat_rows_rule()
stat_cols_rule()
stat_rows_projection()
stat_cols_projection()
- Convenience stats for row and column matrix factors
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as_tbl_ord(<cancor_ord>)
recover_rows(<cancor_ord>)
recover_cols(<cancor_ord>)
recover_inertia(<cancor_ord>)
recover_coord(<cancor_ord>)
recover_conference(<cancor_ord>)
recover_supp_rows(<cancor_ord>)
recover_supp_cols(<cancor_ord>)
recover_aug_rows(<cancor_ord>)
recover_aug_cols(<cancor_ord>)
recover_aug_coord(<cancor_ord>)
- Functionality for canonical correlations
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as_tbl_ord(<cmds_ord>)
recover_rows(<cmds_ord>)
recover_cols(<cmds_ord>)
recover_inertia(<cmds_ord>)
recover_coord(<cmds_ord>)
recover_conference(<cmds_ord>)
recover_aug_rows(<cmds_ord>)
recover_aug_cols(<cmds_ord>)
recover_aug_coord(<cmds_ord>)
- Functionality for classical multidimensional scaling objects
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as_tbl_ord(<correspondence>)
recover_rows(<correspondence>)
recover_cols(<correspondence>)
recover_inertia(<correspondence>)
recover_conference(<correspondence>)
recover_coord(<correspondence>)
recover_aug_rows(<correspondence>)
recover_aug_cols(<correspondence>)
recover_aug_coord(<correspondence>)
- Functionality for correspondence analysis ('correspondence') objects
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as_tbl_ord(<eigen>)
recover_rows(<eigen>)
recover_cols(<eigen>)
recover_inertia(<eigen>)
recover_coord(<eigen>)
recover_conference(<eigen>)
recover_aug_rows(<eigen_ord>)
recover_aug_cols(<eigen_ord>)
recover_aug_coord(<eigen>)
as_tbl_ord(<eigen_ord>)
recover_rows(<eigen_ord>)
recover_cols(<eigen_ord>)
recover_inertia(<eigen_ord>)
recover_coord(<eigen_ord>)
recover_conference(<eigen_ord>)
recover_aug_coord(<eigen_ord>)
- Functionality for eigen-decompositions
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as_tbl_ord(<factanal>)
recover_rows(<factanal>)
recover_cols(<factanal>)
recover_inertia(<factanal>)
recover_coord(<factanal>)
recover_conference(<factanal>)
recover_supp_rows(<factanal>)
recover_aug_rows(<factanal>)
recover_aug_cols(<factanal>)
recover_aug_coord(<factanal>)
- Functionality for factor analysis ('factanal') objects
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as_tbl_ord(<kmeans>)
recover_rows(<kmeans>)
recover_cols(<kmeans>)
recover_coord(<kmeans>)
recover_aug_rows(<kmeans>)
recover_aug_cols(<kmeans>)
recover_aug_coord(<kmeans>)
- Functionality for k-means clustering ('kmeans') objects
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as_tbl_ord(<lda>)
as_tbl_ord(<lda_ord>)
recover_rows(<lda>)
recover_rows(<lda_ord>)
recover_cols(<lda>)
recover_cols(<lda_ord>)
recover_inertia(<lda>)
recover_inertia(<lda_ord>)
recover_coord(<lda>)
recover_coord(<lda_ord>)
recover_conference(<lda>)
recover_conference(<lda_ord>)
recover_aug_rows(<lda>)
recover_aug_rows(<lda_ord>)
recover_aug_cols(<lda>)
recover_aug_cols(<lda_ord>)
recover_aug_coord(<lda>)
recover_aug_coord(<lda_ord>)
recover_supp_rows(<lda>)
recover_supp_rows(<lda_ord>)
- Functionality for linear discriminant analysis ('lda') objects
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as_tbl_ord(<lm>)
recover_rows(<lm>)
recover_cols(<lm>)
recover_coord(<lm>)
recover_aug_rows(<lm>)
recover_aug_cols(<lm>)
recover_aug_coord(<lm>)
recover_aug_rows(<glm>)
recover_rows(<mlm>)
recover_cols(<mlm>)
recover_coord(<mlm>)
recover_aug_rows(<mlm>)
recover_aug_cols(<mlm>)
recover_aug_coord(<mlm>)
- Functionality for linear model objects
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as_tbl_ord(<lra>)
recover_rows(<lra>)
recover_cols(<lra>)
recover_inertia(<lra>)
recover_coord(<lra>)
recover_conference(<lra>)
recover_aug_rows(<lra>)
recover_aug_cols(<lra>)
recover_aug_coord(<lra>)
- Functionality for log-ratio analysis ('lra') objects
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as_tbl_ord(<mca>)
recover_rows(<mca>)
recover_cols(<mca>)
recover_inertia(<mca>)
recover_conference(<mca>)
recover_coord(<mca>)
recover_supp_rows(<mca>)
recover_aug_rows(<mca>)
recover_aug_cols(<mca>)
recover_aug_coord(<mca>)
- Functionality for multiple correspondence analysis ('mca') objects
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as_tbl_ord(<prcomp>)
recover_rows(<prcomp>)
recover_cols(<prcomp>)
recover_inertia(<prcomp>)
recover_coord(<prcomp>)
recover_conference(<prcomp>)
recover_aug_rows(<prcomp>)
recover_aug_cols(<prcomp>)
recover_aug_coord(<prcomp>)
- Functionality for principal components analysis ('prcomp') objects
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as_tbl_ord(<princomp>)
recover_rows(<princomp>)
recover_cols(<princomp>)
recover_inertia(<princomp>)
recover_coord(<princomp>)
recover_conference(<princomp>)
recover_supp_rows(<princomp>)
recover_aug_rows(<princomp>)
recover_aug_cols(<princomp>)
recover_aug_coord(<princomp>)
- Functionality for principal components analysis ('princomp') objects